Plant breeding deals with high-yielding genotypes. However, how best to choose parents of these genotypes remains an unsolved question. Here, we focus on a priori choice based on parental distances by means of agronomic and molecular data. Despite numerous theoretical and empirical studies, a priori choice continues to be a controversial procedure. Both success and failure are commonly reported...

Speciation is the process by which reproductively isolated lineages arise, and is one of the fundamental means by which the diversity of life increases. Whereas numerous studies have documented an association between ecological divergence and reproductive isolation, relatively little is known about the role of natural selection in genome divergence during the process of speciation. Here, we use...

In a recent Frontiers in Neuroscience paper (Neftci et al., 2014) we contributed an on-line learning rule, driven by spike-events in an Integrate and Fire (IF) neural network, that emulates the learning performance of Contrastive Divergence (CD) in an equivalent Restricted Boltzmann Machine (RBM) amenable to real-time implementation in spike-based neuromorphic systems. The eventdriven CD framew...

Synonymous codons are not used at equal frequency throughout the genome, a phenomenon termed codon usage bias (CUB). It is often assumed that interspecific variation in the intensity of CUB is related to species differences in effective population sizes (N e), with selection on CUB operating less efficiently in species with small N e. Here, we specifically ask whether variation in N e predicts ...

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450...

1. Wilcox LM Jr, Gittinger JW Jr, Breinin GM. Congenital adduction palsy and synergistic divergence. Am J Ophthalmol. 1981;91(1):1-7. 2. Kim JH, Hwang JM. Adduction on attempted abduction: the opposite of synergistic divergence. Arch Ophthalmol. 2006;124(6):918-920. 3. Lim KH, Engle EC, Demer JL. Abnormalities of the oculomotor nerve in congenital fibrosis of the extraocular muscles and congeni...

BACKGROUND The quantification of species-richness and species-turnover is essential to effective monitoring of ecosystems. Wetland ecosystems are particularly in need of such monitoring due to their sensitivity to rainfall, water management and other external factors that affect hydrology, soil, and species patterns. A key challenge for environmental scientists is determining the linkage betwee...

Type 1 serine/threonine protein phosphatases (PP1s) play key roles in many cellular processes. To understand the evolutionary relationships among PP1s from various kingdoms and to provide a valid basis to evaluate the structure-function relationships of these phosphatases, 44 PP1 sequences were aligned, revealing a high sequence similarity among PP1 homologs. About one-third of the total amino ...

Contrastive divergence (CD) is a promising method of inference in high dimensional distributions with intractable normalizing constants, however, the theoretical foundations justifying its use are somewhat weak. This document proposes a framework for understanding CD inference, including how and when it works. It provides multiple justifications for the CD moment conditions, including framing t...

We study an expansion of the log likelihood in undirected graphical models such as the restricted Boltzmann machine (RBM), where each term in the expansion is associated with a sample in a Gibbs chain alternating between two random variables (the visible vector and the hidden vector in RBMs). We are particularly interested in estimators of the gradient of the log likelihood obtained through thi...